Did increased gene duplication set the stage for human evolution?

Feb 11, 2009

These are two western lowland gorillas at Woodland Park Zoo, Seattle. This species is from western equatorial African. The gorilla on the left shows the knuckles-on-the-ground stance characteristic of great apes. Credit: Allison C. Gray

(PhysOrg.com) -- Roughly 10 million years ago, a major genetic change occurred in a common ancestor of gorillas, chimpanzees, and humans. Segments of DNA in its genome began to form duplicate copies at a greater rate than in the past, creating an instability that persists in the genome of modern humans and contributes to diseases like autism and schizophrenia. But that gene duplication also may be responsible for a genetic flexibility that has resulted in some uniquely human characteristics.

"Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions," says Howard Hughes Medical Institute investigator and University of Washington geneticist Evan Eichler, who led the project that uncovered the new findings. "These are really like volcanoes in the genome, blowing out pieces of DNA." The research was published in the February 12, 2009, issue of Nature.

Eichler and his colleagues focused on the genomes of four different species: macaques, orangutans, chimpanzees, and humans. All are descended from a single ancestral species that lived about 25 million years ago. The line leading to macaques broke off first, so that macaques are the most distantly related to humans in evolutionary terms. Orangutans, chimpanzees, and humans share a common ancestor that lived 12-16 million years ago. Chimps and humans are descended from a common ancestral species that lived about 6 million years ago.

By comparing the DNA sequences of the four species, Eichler and his colleagues identified gene duplications in the lineages leading to these species since they shared a common ancestor. They also were able to estimate when a duplication occurred from the number of species sharing that duplication. For example, a duplication observed in orangutan, chimpanzees, and humans but not in macaques must have occurred sometime after 25 million years ago but before the orangutan lineage branched off.

Eichler's research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period. "There's a big burst of activity that happens where genomes are suddenly rearranged and changed," he says. Surprisingly, the rate of duplications slowed down again after the lineages leading to humans and to chimpanzees diverged. "You might like to think that humans are special because we have more duplications than did earlier species," he says, "but that's not the case."

These duplications have created regions of our genomes that are especially prone to large-scale reorganizations. "That architecture predisposes to recurrent deletions and duplications that are associated with autism and schizophrenia and with a whole host of other diseases," says Eichler.

Yet these regions also exhibit signs of being under positive selection, meaning that some of the rearrangements must have conferred advantages on the individuals who inherited them. Eichler thinks that uncharacterized genes or regulatory signals in the duplicated regions must have created some sort of reproductive edge. "I believe that the negative selection of these duplications is being outweighed by the selective advantage of having these newly minted genes, but that's still unproven," he said.

An important task for future studies is to identify the genes in these regions and analyze their functions, according to Eichler. "Geneticists have to figure out the genes in these regions and how variation leads to different aspects of the human condition such as disease. Then, they can pass that information on to neuroscientists and physiologist and biochemists who can work out what these proteins are and what they do," he says. "There is the possibility that these genes might be important for language or for aspects of cognition, though much more work has to be done before we'll be able to say that for sure."

More information: Nature, February 12, "A burst of segmental duplications in the genome of the African great ape ancestor"

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Evolution requires that simple genes became more complex genes, with more information. It was NEVER observed! Mutation is just a change in the existing genes. That why evolution is flaw.

Oh dear! It would be so easy to despair sometimes.

Evolution does not "require" any such thing. In many genomes there are simple genes that perform their task perfectly adequately and if a point-mutation should occur in them the organism would be inviable. Further, there is in fact good evidence from a number of researchers studying a variety of organisms' genomes that natural selection favours a reduction in absolute gene length, not an increase. There are a number of possible reasons for this but a couple of potentially good ones are that: during cell division, shorter genes are more likely to be accurately replicated without accumulating deleterious mutations; transcriptional efficiency and protein synthesis efficiency is increased if gene lengths are shorter.

Where natural selection does appear to favour an increase in length and/or complexity is in proteins and this therefore can positively influence increased gene length. There is obviously a trade-off here and gene length cannot arbitrarily increase to an indefinite degree.

In addition, "mutations" occur in a wide range of scales, from single base transposition, to gene or gene-complex multiplication (look up "fragile-x syndrome" for just one example) and on up to replication 2 or more times of the entire genome. In some cases the change is benign and neutral in effect, in some cases it is deleterious and in other cases it is advantageous to the individual concerned. The change, advantageous or not, may or may not get passed on. (e.g. an advantageous mutation doesn't get to the next generation if the individual gets eaten by a predator before reproducing.)

There is no "flaw" in evolution and I suggest you go back to reading your superstition books (giving you the benefit of doubt - I have no idea what religion you profess to follow) rather than attempt reading about science.

Evolution requires that simple genes became more complex genes, with more information. It was NEVER observed!

While malapropism is correct that you are wrong about a requirement for an increase in complexity that isn't only flaw there. Did you actually read the article? It shows you are wrong. Duplication IS an increase in complexity. Therefor it HAS been observed. Not just in this instance either.

When a gene is duplicated that means that it becomes possible for one of the duplications to vary by mutation without the loss of a functioning and needed protein. The gene that changes can then do new things. Which is very much an increase in complexity and it can be seen throughout the genome.

You don't seem to understand the point being made by me and Ethelred - that complexity can be achieved in many different ways. The way that I think you are suggesting is unnecessary and therefore doesn't generally occur (nature may abhor a vacuum but it seems to abhor the unnecessary even more).

To use an analogy, a computer programming language is a very defined set of commands and parameters, none of which might ever vary in scope once they have been first created (i.e. they don't increase in complexity). Nevertheless, by combining these command words and their parameter variations in different ways or increasing the number of them that have been used, or both, we can achieve computer programs that vary from very simple "Hello world" kind of things, to very complex modeling or other applications.

This same sort of thing occurs in genetics. At the simplest level, the set of "letters" used to "program" the construction of an organism (whether considered at species level or individual level, doesn't matter) is very prescribed and never varies. These "letters" do not themselves increase in complexity, ever, because there is no need (and besides, if they did, they wouldn't form complementary codes any longer so the whole construct of genetics would fall apart). Despite this, it is possible, using just these 4 base codes to "construct" organisms in a breathtaking range of complexity. (For clarity: I am using the term "construct" in a metaphorical rather than literal sense, however if you choose to believe in a literal "construction", go ahead; no evidence supports it but I wouldn't deny you your misapprehensions.)

By extension, if this range of organisms can be formed simply by different arrangements of only 4 chemical objects, then it is not necessary to increase the complexity of their products to achieve similar range variations, it is only necessary to generate different combinations or dosages of the same products or to create new products from different variations of the 4 code letters. In general terms, this is in fact what happens.

I hope this has clarified these ideas somewhat.

And finally, what Ethelred last said.

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